Transposable Elements Contribute to Genome-Specific Structural and Functional Variations in Bread Wheat

Transposable elements (TEs), which occupies ~85% of the wheat genome, are a major source for genetic variations in bread wheat. However, the contribution of TEs to structural and functional variations in bread wheat genes is not fully understood. Here, publicly available databases were integrated to identify TE insertions within gene bodies and assess their impact on gene expression variations of homoeologous gene groups in bread wheat. Overall, 70,818 genes were analyzed: 55,170 genes appeared in all three subgenomes, named triads; 12,640 genes appeared only in two subgenomes, named dyads; and 3,008 genes that underwent duplication in a single subgenomes, named tetrads. To this end, we found that ~36% of the 70,818 genes contained at least one TE insertion, mostly in triads. TE insertions were found to be either monomorphic (i.e., found in all the homoeologous copies) or polymorphic (i.e., found only in some of the homoeologous copies), with significant correlation between polymorphism and homoeolog expression bias in dyads and triads. Analysis of 14,258 triads revealed that the presence of TE insertions in at least one of the triad genes correlated to balanced expression of the homoeologous. TE insertions within the exon or the untranslated regions of at least one homoeolog in a triad correlated with homoeolog expression bias. Furthermore, we found correlation between presence\absence of TEs insertions belong to 6 superfamilies and 17 subfamilies and suppression of a single homoeolog. Our findings indicate that TEs might play a prominent role on controlling gene expression in a genome-specific manner in bread wheat.